Holmgren, N. M. A., Norrström, N., Aps, R., and Kuikka, S. 2012. MSY-orientated management of Baltic Sea herring (Clupea harengus) during different ecosystem regimes. – ICES Journal of Marine Science, 69: 257–266. The Baltic Sea ecosystem has undergone dramatic changes, so-called ecosystem regime shifts, during the past four decades. Baltic Sea herring (Clupea harengus) spawning-stock biomass has declined to a third, and weight-at-age has halved as a result of food shortages and competition with sprat (Sprattus sprattus). The management objective for the herring stock is currently in transition from precautionary to maximum sustainable yield (MSY). The main basin Baltic Sea herring was modelled under the current ecosystem regime and the effect of a recovery of the cod (Gadus morhua) stock and the availability of planktonic food to levels found in the early 1980s analysed. A target of FMSY = 0.16 for herring, which should decline to FMSY = 0.10 with recovery of the cod stock, is proposed. An increase in the availability of planktonic food is estimated to more than double the yield at FMSY = 0.27, overriding the negative effects of cod predation should there be a simultaneous increase in both cod and availability of planktonic food. The estimated net increase in yield is 40% at FMSY = 0.20. Functions are presented to calculate FMSY and to estimate the expected yield depending on the abundance of cod and food availability. Retrospective application of the functions is indicative of overfishing of herring in the 1990s and early 2000s, and a net loss in yield, with a landing value of some €440 million.